1. Valkyria Chronicles 4 (Nintendo Switch, PS4, Xbox One, PC)
One aspect none of the other games on this list really deal with is the idea of teenagers being groomed for war. Beyond the fun conversations, tea parties, and dealing with bandits and monsters that is ultimately the purpose of what you are doing in Fire Emblem: Three Houses. You are preparing young people to kill others in war. That’s just a harsh reality of the game.
The only other series I’m aware of to really do this is Valkyria Chronicles. The first game in the series is also available on most platforms, but I’m going to specifically recommend Valkyria Chronicles 4 because as a more modern entry it has some refinements the original simply doesn’t have due to being over a decade old at this point.
In addition, Valkyria Chronicles 4 features turn-based strategy combat, a wide variety of units (though you can’t change out their classes as you go), the possibility of units dying and personal traits and relationships that can affect things on the battlefield. Really, if you were to make a Fire Emblem game that took place in an alternate timeline World War II setting, I’d roughly expect it to be pretty similar to the Valkyria Chronicles series.
Heck, Nintendo seems to be very on board with crossovers and collaborations these days, maybe we can get an actual Fire Emblem/Valkyria Chronicles crossover game. In the meantime, while any game on this list would be a good chaser after being done with Fire Emblem: Three Houses, I really feel Valkyria Chronicles 4 comes closest to nailing the same vibe if that’s what you are after so check it out.